The mcu would do the communication between pixhawk and the motor controller. I guess the plan for this weekend is to see if I can make the mcu understand the signals sent by pixhawk!
I did this some time ago, when ardurover did not support H-bridges.
I used an arduino to read two PWM channels and generated the PWM + two digital outputs with it.
There are many examples how to read PWM signals. With modern 32bit MCUs it should be easier than with an arduino, because they have more interrupts. But an arduino should still be enough.
To be honest, I haven’t used proper arduinos in some time, I have plenty other microcontrollers 
Well if it’s possible in theory it’s definitively how I’m spending part of my weekend !
Thanks!